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⚡ Bolt: vectorize griddata_v4 in topoplot#288

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⚡ Bolt: vectorize griddata_v4 in topoplot#288
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💡 What: Replaced the slow double-nested Python loop inside the biharmonic spline interpolation helper griddata_v4 with fully vectorized NumPy operations.
🎯 Why: In EEG topographic plotting (topoplot), griddata_v4 was heavily bottlenecked by a double loop running $M \times N$ iterations (e.g. 67x67 = 4489 iterations) inside Python.
📊 Impact: Decreased the average execution time of griddata_v4 by ~85% (from ~75.79 ms to ~11.40 ms, equivalent to a ~6.6x speedup).
🔬 Measurement: Verified using a temporary benchmark script tools/benchmark_topoplot.py and confirmed correctness with the existing unit test suite in tests/test_topoplot.py.


PR created automatically by Jules for task 3404990960757105469 started by @suraj-ranganath

Replaced the double-nested loop over query coordinate grids (size m x n) in `griddata_v4` with vectorized NumPy broadcasting operations and matrix-vector multiplication (`@`). This optimizes biharmonic spline interpolation for topographic plotting, resulting in a ~6.6x performance speedup (execution time reduced from ~75.79 ms to ~11.40 ms for a typical 67x67 grid with 64 channels) with 100% numerical correctness.

Co-authored-by: suraj-ranganath <14310165+suraj-ranganath@users.noreply.github.com>
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@claude

claude Bot commented Jul 18, 2026

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Claude finished @suraj-ranganath's task in 1m 46s —— View job


PR Review: vectorize griddata_v4 in topoplot

  • Read the diff
  • Verify numerical equivalence of the vectorization
  • Check existing test coverage
  • Post review

Verdict: Looks correct and is a clean, worthwhile optimization.

The rewrite is mathematically equivalent to the original double loop, and the change is well-covered by the existing tests/test_topoplot.py suite (test_zero_distance_handling, test_collinear_points, and the test_parity_* MATLAB-parity tests all exercise this path).

Equivalence check (by inspection)

The old per-point loop and the new vectorized form produce identical results:

  • Old: for each grid point, d = |xq[i,j] + 1j*yq[i,j] − xy|g = d²(log d − 1)g[d==0]=0vq[i,j] = g·weights.
  • New: d = |q_flat[:,None] − xy[None,:]| builds the full (N_query, N_known) distance matrix, applies the same Green's function and zero-distance fix, then (g @ weights).reshape(xq.shape).

Two details that are handled correctly:

  • The old code reassigned xy = xy[:, None] before the loop; the new code correctly drops that reassignment and uses the original 1D xy in xy[np.newaxis, :]. 👍
  • ravel() and reshape(xq.shape) both default to C-order, so the flatten/unflatten round-trip preserves grid layout. Correct.

Minor notes (non-blocking)

  1. Memory tradeoff worth a comment. The vectorized form materializes two full (N_query, N_known) matrices (d and g) instead of one row at a time. For the default GRID_SCALE = 67 (~4.5k query points) this is trivial. But topoplot accepts a user-supplied gridscale; at e.g. 300×300 (90k points) × a few hundred channels this is a couple hundred MB per array. That's an acceptable tradeoff for the ~6.6× speedup, but a one-line comment noting the peak allocation would help future readers who bump gridscale.

  2. .jules/bolt.md committed to the repo. This agent-journal file is included in the PR. Per the repo's convention of keeping dev/tooling artifacts out of the package (the PR body notes the benchmark script was intentionally not committed), consider whether this should be committed or added to .gitignore instead. Cosmetic only, but its header date (2025-02-17) also predates the actual work.

  3. No new test needed. Since this is a pure refactor with unchanged behavior, relying on the existing suite is the right call — no redundant test required.

Nice work — the speedup is real and the correctness is preserved.
• Branch: jules-3404990960757105469-970b341e

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🤖 Closing as a duplicate of #263. Flattening the query grid before the broadcast is only a layout variation of the already-vetted vectorization in #263, with the same numerical and memory complexity. #263 is cleaner and this PR also commits the unrelated .jules/bolt.md artifact, so there is no benefit to keeping both.

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